Find loops using chromosight
getLoops(
x,
resolution = NULL,
output_prefix = file.path("chromosight", "chromo"),
norm = "auto",
max.dist = "auto",
min.dist = "auto",
min.separation = "auto",
n.mads = 5L,
pearson = "auto",
nreads = "no",
ncores = 1L
)A HiCExperiment object
Which resolution to use to search loops
Prefix to chromosight output (default: "chromosight/chromo")
Normalization parameter for chromosight
Min and max distance to use to filter for significant loops
Minimum separation between anchors of potential loops
Number of MADs to use to filter relevant bins to search for loops
Minimum Pearson correlation score to use to filter for significant loops
Number of reads to subsample to before searching for loops
Number of cores for chromosight
A HiCExperiment object with a new "loops" topologicalFeatures
storing significant interactions identified by chromosight, and an additional
chromosight_args metadata entry.
contacts_yeast <- contacts_yeast()
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
contacts_yeast <- getLoops(contacts_yeast)
S4Vectors::metadata(contacts_yeast)$chromosight_args
#> $`--pattern`
#> [1] "loops"
#>
#> $`--dump`
#> [1] "/tmp/RtmpHqc8oD"
#>
#> $`--inter`
#> [1] FALSE
#>
#> $`--iterations`
#> [1] "auto"
#>
#> $`--kernel-config`
#> NULL
#>
#> $`--perc-zero`
#> [1] "auto"
#>
#> $`--perc-undetected`
#> [1] "auto"
#>
#> $`--tsvd`
#> [1] FALSE
#>
#> $`--win-fmt`
#> [1] "json"
#>
#> $`--win-size`
#> [1] "auto"
#>
#> $`--no-plotting`
#> [1] TRUE
#>
#> $`--smooth-trend`
#> [1] FALSE
#>
#> $`--norm`
#> [1] "auto"
#>
#> $`<contact_map>`
#> [1] "/github/home/.cache/R/ExperimentHub/1ee414121583_7752::/resolutions/16000"
#>
#> $`--max-dist`
#> [1] "auto"
#>
#> $`--min-dist`
#> [1] "auto"
#>
#> $`--min-separation`
#> [1] "auto"
#>
#> $`--n-mads`
#> [1] 5
#>
#> $`<prefix>`
#> [1] "chromosight/chromo"
#>
#> $`--pearson`
#> [1] "auto"
#>
#> $`--subsample`
#> [1] "no"
#>
#> $`--threads`
#> [1] 1
#>
topologicalFeatures(contacts_yeast, 'loops')
#> GInteractions object with 53 interactions and 5 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2 | bin_id1
#> <Rle> <IRanges> <Rle> <IRanges> | <numeric>
#> [1] II 16001-32000 --- II 416001-432000 | 16
#> [2] II 16001-32000 --- II 624001-640000 | 16
#> [3] II 160001-176000 --- II 336001-352000 | 25
#> [4] II 432001-448000 --- II 576001-592000 | 42
#> [5] III 16001-32000 --- III 176001-192000 | 67
#> ... ... ... ... ... ... . ...
#> [49] XVI 16001-32000 --- XVI 272001-288000 | 704
#> [50] XVI 304001-320000 --- XVI 384001-400000 | 722
#> [51] XVI 400001-416000 --- XVI 672001-688000 | 728
#> [52] XVI 720001-736000 --- XVI 928001-944000 | 748
#> [53] XVI 704001-720000 --- XVI 768001-784000 | 747
#> bin_id2 score pvalue qvalue
#> <numeric> <numeric> <numeric> <numeric>
#> [1] 41 0.367443 6.316e-07 6.832e-07
#> [2] 54 0.420304 7.000e-09 9.600e-09
#> [3] 36 0.492732 0.000e+00 0.000e+00
#> [4] 51 0.417455 0.000e+00 0.000e+00
#> [5] 77 0.458787 2.100e-09 3.100e-09
#> ... ... ... ... ...
#> [49] 720 0.587076 0.000e+00 0.000e+00
#> [50] 727 0.326277 5.085e-07 5.734e-07
#> [51] 745 0.601166 0.000e+00 0.000e+00
#> [52] 761 0.567326 0.000e+00 0.000e+00
#> [53] 751 0.333732 5.591e-07 6.174e-07
#> -------
#> regions: 98 ranges and 0 metadata columns
#> seqinfo: 14 sequences from an unspecified genome; no seqlengths